Sorry to hear you’ve been having trouble with this!
Honestly, based on your description it sounds like that one taxonomic assignment might just be all that’s in your samples (though it is suspicious). Here’s the key:
Thanks for doing that test! So we know the classifier works…
You could also try using one of the pre-trained full-length 16S classifiers distributed on the website to get a “second opinion” — if you get a more satisfying result I’d say just use that (trimming to your primers only gives a slight boost in performance anyway).
It is possible to have different features receive the same taxonomy classification. Distinct features are just unique sequences here, and do not necessarily have different taxonomic affiliations. Though 1606 features receiving the same classification is quite suspicious.
If using one of the pre-trained classifiers does not fix your issue, would you mind sharing the following files?
- rep-set.qza + qzv
Also please try
qiime taxa barplot and share that file.